Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6A

Orthogroup ID

OG0003037

Physical Location & Seq

Genomic Coordinates Reverse (-)

23486216 .. 23490071

Gene Structure 3856 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6AG149200.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 648 bp

ATGCAGGCAGATGCCCTTGAATCTCCACCTCCGTGGCTACTGATCGACTGCGATTTATATTTGAAGAAGAAAAGCAGGATTAGCAGGTGGTCTGCTCTGTTGTACTTGTCCACACTGAGGGGTCATATCCGTCAAAAGCTCAAATCAAAATGGAGGAATACCCTGACAGCTTGGGGTAATGAGAAGGAATTTGTTGAGGATGCTGCAAAGGAGTATGATGAGAGTACTATTACTTGTGCTTCAGAACTCGGGCTGCTGGAGCAAAATGCCAAAGAGAAGTTGCTCTTTGTTCAGTTGCCTCCTACTCTACCATTGGTCAAGCGACCAACTAGTGCAAAGGGGAAAGAGAAAGTCGGAAGCTCAGCACCATCAGAGAAGGTAGGTGCTGCAAGGAAGGGCGGTAGTTTGGAAGAGTTATCTGAGGGGTATGTGGGGAAGAAGCTGATTTACAAGAGTGGAGCAGTCAAGTTCAAAATAGGAGATGCACTGTATGATGTTTCACCCGGTTCAGATTGTATATTTGCTCAAGATGTTGCTGCAATCAACACTGCAGTGAGAAAGTGTTGTGTTCTTGGAGAGCTTGGCCAGCAAGTTGTTATAACTCCTGATGTGGATTCCCTACTAGACGCAACGATTGAGTTGGACTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0001817 GO:0001819 GO:0002682 GO:0002684 GO:0003674 GO:0003682 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0005737 GO:0005829 GO:0008150 GO:0016604 GO:0016607 GO:0030880 GO:0031347 GO:0031349 GO:0031974 GO:0031981 GO:0032479 GO:0032481 GO:0032648 GO:0032728 GO:0032991 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044446 GO:0044451 GO:0044464 GO:0045088 GO:0045089 GO:0048518 GO:0048583 GO:0048584 GO:0050776 GO:0050778 GO:0050789 GO:0051239 GO:0051240 GO:0055029 GO:0061695 GO:0065007 GO:0070013 GO:0080134 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko04623 ko05169 map00230 map00240 map01100 map03020 map04623 map05169

Pfam Domains

Protein Families

RNA_pol_Rpc4

Protein Analysis

215

Amino Acids

23.54

Weight (kDa)

7.54

Isoelectric Point (pI)

36.13

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpc4	PF05132	92 - 204	2.8e-23	RNA polymerase III RPC4

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Publication-ready

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Orthologous Genes (Group: OG0003037)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G09380 AT5G09380 AT5G09380
fragaria_vesca	FvH4_1g08400 FvH4_1g08400 FvH4_7g27240 FvH4_7g27240
malus_domestica	MD01G1181300.v1.1 MD02G1088300.v1.1 MD07G1251400.v1.1
prunus_persica	Prupe.2G275200_v2.0.a1 Prupe.7G201300_v2.0.a1
pyrus_communis	pycom02g07090 pycom07g22410
rosa_chinensis	RchiOBHm_Chr1g0374021 RchiOBHm_Chr2g0094511 RchiOBHm_Chr3g0487921
rosa_laevigata	RLG00000016497 RLG00000026785
rosa_multiflora	Rmu_sc0004359.1_g000044 Rmu_sc0006924.1_g000006 Rmu_sc0009793.1_g000002
rosa_roxburghii	Rroxscaffold_2G00147110 Rroxscaffold_4G00283820
rosa_rugosa	Rorug01G0380300 Rorug02G0044300.1
rosa_samantha	Rh1AG390800 Rh1BG354900 Rh1CG368000 Rh1DG385600 Rh2AG092600 Rh2BG092800 Rh2CG095300 Rh2DG091700 Rh3AG285100 Rh6AG149200
rosa_wichuraiana	Rw1G034440 Rw6G012910

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	599
AarI	CACCTGC	1 cut(s)	75
Acc36I	ACCTGC	1 cut(s)	75
AciI	CCGC	1 cut(s)	399
AcoI	YGGCCR	1 cut(s)	583
AcsI	RAATTY	1 cut(s)	188
AcuI	CTGAAG	1 cut(s)	225
AfaI	GTAC	2 cut(s)	104, 226
AfiI	CCNNNNNNNGG	1 cut(s)	117
AgsI	TTSAA	3 cut(s)	20, 64, 472
AhlI	ACTAGT	1 cut(s)	329
AleI	CACNNNNGTG	2 cut(s)	31, 551
AluBI	AGCT	5 cut(s)	139, 170, 360, 442, 580
AluI	AGCT	5 cut(s)	139, 170, 360, 442, 580
Ama87I	CYCGRG	1 cut(s)	248
AoxI	GGCC	1 cut(s)	583
ApeKI	GCWGC	4 cut(s)	203, 253, 386, 536
ApoI	RAATTY	1 cut(s)	188
AsuC2I	CCSGG	1 cut(s)	504
AsuHPI	GGTGA	1 cut(s)	492
AvaI	CYCGRG	1 cut(s)	248
BalI	TGGCCA	1 cut(s)	585
BarI	GAAGNNNNNNTAC	2 cut(s)	431, 463
BbvI	GCAGC	4 cut(s)	190, 240, 373, 523
BccI	CCATC	1 cut(s)	376
BcnI	CCSGG	1 cut(s)	504
BcuI	ACTAGT	1 cut(s)	329
BfaI	CTAG	2 cut(s)	330, 623
BfmI	CTRYAG	1 cut(s)	549
BfuAI	ACCTGC	1 cut(s)	75
BisI	GCNGC	4 cut(s)	204, 254, 387, 537
BlpI	GCTNAGC	1 cut(s)	361
BlsI	GCNGC	4 cut(s)	205, 255, 388, 538
BmcAI	AGTACT	1 cut(s)	226
Bme1390I	CCNGG	1 cut(s)	504
BmeT110I	CYCGRG	1 cut(s)	248
BmrFI	CCNGG	1 cut(s)	504
BmsI	GCATC	2 cut(s)	190, 472
BpmI	CTGGAG	1 cut(s)	278
Bpu1102I	GCTNAGC	1 cut(s)	361
BpuEI	CTTGAG	1 cut(s)	510
BpuMI	CCSGG	1 cut(s)	504
BsaJI	CCNNGG	1 cut(s)	32
Bsc4I	CCNNNNNNNGG	1 cut(s)	117
BseDI	CCNNGG	1 cut(s)	32
BseGI	GGATG	1 cut(s)	205
BseLI	CCNNNNNNNGG	1 cut(s)	117
BseMII	CTCAG	3 cut(s)	107, 375, 411
BseXI	GCAGC	4 cut(s)	190, 240, 373, 523
BshFI	GGCC	1 cut(s)	585
BsiHKCI	CYCGRG	1 cut(s)	248
BsiSI	CCGG	1 cut(s)	504
BslI	CCNNNNNNNGG	1 cut(s)	117
BsnI	GGCC	1 cut(s)	585
BsoBI	CYCGRG	1 cut(s)	248
Bsp143I	GATC	1 cut(s)	42
Bsp1720I	GCTNAGC	1 cut(s)	361
BspACI	CCGC	1 cut(s)	399
BspANI	GGCC	1 cut(s)	585
BspCNI	CTCAG	3 cut(s)	108, 374, 412
BspMAI	CTGCAG	1 cut(s)	553
BspMI	ACCTGC	1 cut(s)	75
BssECI	CCNNGG	1 cut(s)	32
BssMI	GATC	1 cut(s)	42
Bst4CI	ACNGT	1 cut(s)	489
Bst6I	CTCTTC	1 cut(s)	405
BstC8I	GCNNGC	2 cut(s)	6, 587
BstDEI	CTNAG	3 cut(s)	116, 361, 420
BstDSI	CCRYGG	1 cut(s)	32
BstF5I	GGATG	1 cut(s)	205
BstKTI	GATC	1 cut(s)	45
BstMBI	GATC	1 cut(s)	42
BstMWI	GCNNNNNNNGC	3 cut(s)	81, 259, 586
BstSCI	CCNGG	1 cut(s)	502
BstSFI	CTRYAG	1 cut(s)	549
BstV1I	GCAGC	4 cut(s)	190, 240, 373, 523
BstXI	CCANNNNNNTGG	1 cut(s)	33
BsuRI	GGCC	1 cut(s)	585
BtgI	CCRYGG	1 cut(s)	32
BtsCI	GGATG	1 cut(s)	205
BtsI	GCAGTG	2 cut(s)	546, 558
BtsIMutI	CAGTG	4 cut(s)	113, 485, 546, 558
BveI	ACCTGC	1 cut(s)	75
Cac8I	GCNNGC	2 cut(s)	6, 587
CseI	GACGC	1 cut(s)	635
Csp6I	GTAC	2 cut(s)	103, 225
CviJI	RGCY	8 cut(s)	37, 139, 170, 253, 360, 442, 580, 585
CviKI_1	RGCY	8 cut(s)	37, 139, 170, 253, 360, 442, 580, 585
CviQI	GTAC	2 cut(s)	103, 225
DdeI	CTNAG	3 cut(s)	116, 361, 420
DpnI	GATC	1 cut(s)	44
DpnII	GATC	1 cut(s)	42
EaeI	YGGCCR	1 cut(s)	583
Eam1104I	CTCTTC	1 cut(s)	405
EarI	CTCTTC	1 cut(s)	405
Eco57I	CTGAAG	1 cut(s)	225
Eco88I	CYCGRG	1 cut(s)	248
FaiI	YATR	7 cut(s)	58, 126, 216, 429, 492, 518, 599
FalI	AAGNNNNNCTT	2 cut(s)	269, 301
Fnu4HI	GCNGC	4 cut(s)	204, 254, 387, 537
FokI	GGATG	1 cut(s)	212
Fsp4HI	GCNGC	4 cut(s)	204, 254, 387, 537
FspBI	CTAG	2 cut(s)	330, 623
GluI	GCNGC	4 cut(s)	204, 254, 387, 537
GsuI	CTGGAG	1 cut(s)	278
HaeIII	GGCC	1 cut(s)	585
HapII	CCGG	1 cut(s)	504
HgaI	GACGC	1 cut(s)	635
HinfI	GANTC	2 cut(s)	20, 614
HpaII	CCGG	1 cut(s)	504
HphI	GGTGA	1 cut(s)	492
Hpy166II	GTNNAC	1 cut(s)	111
Hpy188I	TCNGA	5 cut(s)	244, 356, 373, 421, 511
Hpy188III	TCNNGA	2 cut(s)	527, 605
Hpy8I	GTNNAC	1 cut(s)	111
HpyAV	CCTTC	3 cut(s)	178, 370, 388
HpyCH4III	ACNGT	1 cut(s)	489
HpyCH4V	TGCA	7 cut(s)	4, 206, 335, 389, 485, 539, 551
HpyF10VI	GCNNNNNNNGC	3 cut(s)	81, 259, 586
HpyF3I	CTNAG	3 cut(s)	116, 361, 420
Kzo9I	GATC	1 cut(s)	42
LmnI	GCTCC	2 cut(s)	259, 458
LpnPI	CCDG	7 cut(s)	61, 70, 176, 242, 517, 599, 618
Lsp1109I	GCAGC	4 cut(s)	190, 240, 373, 523
LweI	GCATC	2 cut(s)	190, 472
MaeI	CTAG	2 cut(s)	330, 623
MalI	GATC	1 cut(s)	44
MboI	GATC	1 cut(s)	42
MboII	GAAGA	4 cut(s)	76, 79, 422, 448
MlsI	TGGCCA	1 cut(s)	585
MluCI	AATT	1 cut(s)	188
MluNI	TGGCCA	1 cut(s)	585
MmeI	TCCRAC	2 cut(s)	334, 621
MnlI	CCTC	6 cut(s)	39, 111, 147, 190, 309, 415
Mox20I	TGGCCA	1 cut(s)	585
MscI	TGGCCA	1 cut(s)	585
MslI	CAYNNNNRTG	2 cut(s)	31, 551
Msp20I	TGGCCA	1 cut(s)	585
MspI	CCGG	1 cut(s)	504
MspR9I	CCNGG	1 cut(s)	504
MwoI	GCNNNNNNNGC	3 cut(s)	81, 259, 586
NciI	CCSGG	1 cut(s)	504
NdeII	GATC	1 cut(s)	42
OliI	CACNNNNGTG	2 cut(s)	31, 551
PaqCI	CACCTGC	1 cut(s)	75
PfeI	GAWTC	2 cut(s)	20, 614
PkrI	GCNGC	4 cut(s)	205, 255, 388, 538
PsiI	TTATAA	1 cut(s)	599
PstI	CTGCAG	1 cut(s)	553
RsaI	GTAC	2 cut(s)	104, 226
RsaNI	GTAC	2 cut(s)	103, 225
RseI	CAYNNNNRTG	2 cut(s)	31, 551
SatI	GCNGC	4 cut(s)	204, 254, 387, 537
Sau3AI	GATC	1 cut(s)	42
ScaI	AGTACT	1 cut(s)	226
ScrFI	CCNGG	1 cut(s)	504
SetI	ASST	9 cut(s)	31, 89, 141, 172, 362, 381, 385, 444, 582
SfaNI	GCATC	2 cut(s)	190, 472
SfcI	CTRYAG	1 cut(s)	549
SmiMI	CAYNNNNRTG	2 cut(s)	31, 551
SmlI	CTYRAG	1 cut(s)	525
SmoI	CTYRAG	1 cut(s)	525
SpeI	ACTAGT	1 cut(s)	329
Sse9I	AATT	1 cut(s)	188
SsiI	CCGC	1 cut(s)	399
SspMI	CTAG	2 cut(s)	330, 623
StyD4I	CCNGG	1 cut(s)	502
TaaI	ACNGT	1 cut(s)	489
TaqI	TCGA	1 cut(s)	45
TasI	AATT	1 cut(s)	188
TatI	WGTACW	2 cut(s)	102, 224
TfiI	GAWTC	2 cut(s)	20, 614
TscAI	CASTG	4 cut(s)	120, 492, 553, 558
TseI	GCWGC	4 cut(s)	203, 253, 386, 536
TspGWI	ACGGA	2 cut(s)	21, 119
TspRI	CASTG	4 cut(s)	120, 492, 553, 558
XapI	RAATTY	1 cut(s)	188
XspI	CTAG	2 cut(s)	330, 623
ZrmI	AGTACT	1 cut(s)	226

Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.